Extracellular Action Potential Simulations (EAPS)
NEURON ModelDB Accession: 84589 http://senselab.med.yale.edu/ModelDB/sh ... odel=84589
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Have everything needed.
Loaded in the software, done all the misc trimmings needed for windows (XP)
NOTE: do not use the recommended start-up command:c:\nrn59\bin\neuron.exe -dll mod\nrnmech.dll hoc/src/refs.hoc cells/d151.hoc hoc/src/file_util.hoc hoc/src/main.hoc
I modified it to....
c:\nrn71\bin\neuron.exe -dll mod/nrnmech.dll hoc/src/refs.hoc cells/d151.hoc hoc/src/file_util.hoc hoc/src/main.hoc
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When you run it it fails badly, killing neuron and leaves files open/hung and does a stack dump file nrniv.exe.stackdump
Neuron window contents are below.
It seems to be main.hoc which falls over due to some LOCAL declarations and somehow it gets tied in knots over brace matching....

The originators GOLD, HOLT etc are all out of the picture... but I will approach them if I have to.
meanwhile.... If there's anyone out there who's used it I'd be very grateful for a little guidance. Surely I can't be the first person to use it!
regards,
Colin Hales (see below)
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NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

Colin Hales,
Thanks for bringing this to our attention. We try to test models in modeldb to verify they run. In some cases (commercial applications or special platforms required) the models are not verified.
This one apparently slipped through the cracks as I was able to reproduce the errors you found. I corrected local definition duplications in two files (see below diff) and uploaded the corrected model which ran OK with the first example from the documentation.
-Tom Morse
ModelDB Administrator
PS: This below diff shows that we simply eliminated the duplicated local definitions in the two files
eaps/hoc/src/membrane_init.hoc
eaps/hoc/src/current_util.hoc

Hello again,
All is well. But I have one final question which I am finding troublesome to answer.
Probably a newby question... but better to be sure!
Below is a procedure in the EAPS file current_util( ).
In this program there are roughly 17 different mechanisms.
The program totals up currents by ion type (and pas and cap ... 5 currents in all)
In the case of, say, K, we have, for the current compartment

Question: if there are, say, 6 different mechanisms for this compartment, then exactly how/where does the function ik($1) total up all the K currents for all the different mechanisms?
I cannot fund this function anywhere. I can find the MODL statements for the "ik" for all the relevant channels. But not the function ik(.). I am assuming it is built in, but I can't find it or any docs telling me about it

Read currents from current section into the globals, and add each one
to itot_comp. This is done fore sodium, potassium, calcium, capactive
and passive currents.

IMPORTANT: Chlorine and non ion-specific currents other than the
passive mechanism are not included here! If your model includes
chlorine currents, synapses, shunts or any other mechanism not based
explicitly on sodium, potassium or calcium you must modify this method
to correctly calculate itot_comp!

Note that i * 1e-2 * area(x) converts from mA/cm^2 --> nA

Also note that this is never called for x=0/1 (where there is no
membrane current defined.)

$1 = X for the current compartment
*/

proc read_compartment_currents() {

//--------------------------------------
// Add up different types of ion currents